Read data

source(paste0(root.dir, 'scripts/myRLib.R'))
funcset <- readLines(paste0(root.dir, 'output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/sig_subset.set'))
funcset <- parseFuncSet(funcset)
funcset.names <- names(funcset)
xtyi.files <- strsplit('output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e+00.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-04.assoc.logistic:output-direction_XT_YI/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
ps <- strsplit('1,0.3,0.1,0.03,0.01,0.003,0.001,0.0003,0.0001', ',')[[1]]
inter.files <- strsplit('output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e+00.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-04.assoc.logistic:output-run_step2/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
prs.files <- strsplit('../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e+00.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-01.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-01.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-02.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-02.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-03.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-03.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-04.txt:../step1/output-run_step1/MAGNETIC_HDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-04.txt', ':')[[1]]

Epistasis

for (i in 1:length(xtyi.files)) {
    cat("##", funcset.names[i])
    cat("
")
    cat("
")
    snp.subset <- funcset[[funcset.names[i]]]
    
    # read I ~ SNP
    prs <- read.table(paste0(root.dir, prs.files[i]), header = T)
    prs$sid <- as.character(prs$sid)
    prs.sub <- prs[prs$sid %in% snp.subset, ]
    
    # read others
    xtyi <- read.table(paste0(root.dir, xtyi.files[i]), header = T)
    xtyi$SNP <- as.character(xtyi$SNP)
    yt.xtyi <- xtyi[(xtyi$SNP %in% snp.subset) & (xtyi$SNP %in% 
        prs.sub$sid), ]
    yt.xtyi.xt <- yt.xtyi[yt.xtyi$TEST == "ADD", ]
    yt.xtyi.yi <- yt.xtyi[yt.xtyi$TEST == "PRS", ]
    inter <- read.table(paste0(root.dir, inter.files[i]), header = T)
    inter$SNP <- as.character(inter$SNP)
    inter <- inter[inter$TEST == "ADDxPRS", ]
    yt.inter <- inter[(inter$SNP %in% snp.subset) & (inter$SNP %in% 
        prs.sub$sid), ]
    
    # order all rows
    yt.xtyi.xt <- yt.xtyi.xt[order(yt.xtyi.xt$SNP), ]
    yt.xtyi.yi <- yt.xtyi.yi[order(yt.xtyi.yi$SNP), ]
    yt.inter <- yt.inter[order(yt.inter$SNP), ]
    prs.sub <- prs.sub[order(prs.sub$sid), ]
    
    # check direction
    prs.sub$nt1 <- as.character(prs.sub$nt1)
    yt.xtyi.xt$A1 <- as.character(yt.xtyi.xt$A1)
    yt.inter$A1 <- as.character(yt.inter$A1)
    if (sum(prs.sub$nt1 != yt.xtyi.xt$A1) != 0 | sum(prs.sub$nt1 != 
        yt.inter$A1) != 0) {
        print("Direction does not match. Exit!")
        quit()
    }
    
    yt.xtyi.xt.mean.std <- getMeanStd(yt.xtyi.xt$SNP, yt.xtyi.xt$P, 
        yt.xtyi.xt$OR, "Y~Gi+I (Gi)")
    yt.xtyi.yi.mean.std <- getMeanStd(yt.xtyi.yi$SNP, yt.xtyi.yi$P, 
        yt.xtyi.yi$OR, "Y~Gi+I (I)")
    yt.inter.mean.std <- getMeanStd(yt.inter$SNP, yt.inter$P, 
        yt.inter$OR, "Y~Gi*I")
    prs.sub.mean.std <- data.frame(SNP = prs.sub$sid, Mean = prs.sub$ldpred_beta, 
        Std = 0, Type = "I~Gi")
    
    # create data frame for plot
    df <- rbind(yt.xtyi.xt.mean.std, yt.xtyi.yi.mean.std, prs.sub.mean.std, 
        yt.inter.mean.std)
    ratio <- max(1, nrow(yt.inter)/40)
    cat
    p <- ggplot(df) + geom_point(aes(x = SNP, y = Mean)) + geom_errorbar(aes(x = SNP, 
        ymin = Mean - 1.96 * Std, ymax = Mean + 1.96 * Std), 
        colour = "black", width = 0.1) + geom_hline(yintercept = 0, 
        color = "red") + facet_grid(. ~ Type, scales = "free_x") + 
        coord_flip() + theme(axis.text.x = element_text(angle = 90, 
        hjust = 1))
    p2 <- ggplot(yt.inter) + geom_bar(aes(x = SNP, y = -log10(P)), 
        stat = "identity") + coord_flip() + ggtitle("Interaction P-value")
    subchunkify(p, ratio)
    subchunkify(p2, ratio)
    cat("
")
    inter.plus.gwas.pval <- cbind(yt.inter, yt.xtyi.xt$P)
    colnames(inter.plus.gwas.pval) <- c(colnames(yt.inter), "GWAS.P")
    pander(inter.plus.gwas.pval[order(inter.plus.gwas.pval$P, 
        decreasing = F), ])
    cat("
")
    cat("
")
}

p1.0000e+00

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
36 5 rs449650 0 T ADDxPRS 4864 0.6756 -2.492 0.0127 6.231e-06
39 5 rs436495 0 A ADDxPRS 4864 0.685 -2.417 0.01566 8.586e-06
42 5 rs565928 0 T ADDxPRS 4864 0.6909 -2.36 0.01827 6.713e-06
117 12 rs2167512 0 A ADDxPRS 4864 0.589 -2.341 0.01922 2.471e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.3 1.864 0.06238 3.825e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.752 -1.721 0.08527 2.941e-05
114 12 rs2398486 0 T ADDxPRS 4864 0.6965 -1.665 0.09588 3.649e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.7983 -1.573 0.1157 7.677e-06
144 20 rs2093154 0 T ADDxPRS 4864 1.237 1.509 0.1314 3.405e-05
141 20 rs6071469 0 C ADDxPRS 4864 1.235 1.498 0.1342 3.378e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.244 1.36 0.1737 3.514e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.8332 -1.353 0.1759 4.308e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.8618 -1.158 0.247 4.714e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.129 0.927 0.3539 3.287e-05
60 9 rs523096 0 G ADDxPRS 4864 1.123 0.9074 0.3642 1.46e-06
84 9 rs7865618 0 G ADDxPRS 4864 1.122 0.8902 0.3734 1.484e-09
3 1 rs10914783 0 A ADDxPRS 4864 1.289 0.8606 0.3895 3.316e-06
135 19 rs7250581 0 A ADDxPRS 4864 1.129 0.7636 0.4451 1.187e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.098 0.7272 0.4671 6.903e-14
81 9 rs564398 0 C ADDxPRS 4864 1.098 0.7234 0.4694 9.865e-09
6 1 rs599839 0 G ADDxPRS 4864 1.109 0.6558 0.5119 2.342e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9204 -0.6441 0.5195 7.865e-11
66 9 rs10757264 0 G ADDxPRS 4864 0.922 -0.6308 0.5282 2.255e-07
147 21 rs2838756 0 C ADDxPRS 4864 1.084 0.5678 0.5702 2.722e-05
150 22 rs688034 0 T ADDxPRS 4864 1.076 0.5334 0.5938 1.109e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.057 0.4384 0.6611 3.421e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.055 0.4172 0.6765 7.34e-13
126 16 rs7199903 0 T ADDxPRS 4864 0.9478 -0.4128 0.6798 2.142e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.054 0.4076 0.6836 1.737e-12
105 9 rs1333048 0 A ADDxPRS 4864 1.053 0.4027 0.6872 1.255e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.053 0.3995 0.6895 6.473e-13
78 9 rs10965215 0 A ADDxPRS 4864 0.9568 -0.3431 0.7315 5.374e-10
75 9 rs7049105 0 G ADDxPRS 4864 0.9619 -0.3025 0.7623 1.312e-09
30 4 rs11939435 0 G ADDxPRS 4864 0.9644 -0.1788 0.8581 3.25e-05
54 8 rs16872634 0 C ADDxPRS 4864 0.975 -0.1769 0.8596 4.221e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9775 -0.1569 0.8753 1.262e-05
12 1 rs2133189 0 C ADDxPRS 4864 1.011 0.07838 0.9375 1.416e-05
21 2 rs2943634 0 A ADDxPRS 4864 0.9935 -0.04757 0.9621 1.378e-05

p3.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
36 5 rs449650 0 T ADDxPRS 4864 0.6892 -2.406 0.01611 6.235e-06
117 12 rs2167512 0 A ADDxPRS 4864 0.5882 -2.377 0.01745 2.447e-05
39 5 rs436495 0 A ADDxPRS 4864 0.6978 -2.338 0.01937 8.597e-06
42 5 rs565928 0 T ADDxPRS 4864 0.7041 -2.278 0.02273 6.726e-06
114 12 rs2398486 0 T ADDxPRS 4864 0.694 -1.705 0.08818 3.635e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.7603 -1.677 0.09356 2.921e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.26 1.667 0.09556 3.75e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.8265 -1.433 0.1517 4.227e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.8174 -1.425 0.1542 7.843e-06
144 20 rs2093154 0 T ADDxPRS 4864 1.209 1.369 0.1709 3.342e-05
141 20 rs6071469 0 C ADDxPRS 4864 1.207 1.355 0.1754 3.317e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.227 1.291 0.1968 3.513e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.137 1.01 0.3123 1.489e-09
60 9 rs523096 0 G ADDxPRS 4864 1.136 1.009 0.3132 1.457e-06
132 17 rs6502872 0 T ADDxPRS 4864 0.8812 -1 0.3171 4.731e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.129 0.9449 0.3447 3.319e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.118 0.8767 0.3807 6.881e-14
135 19 rs7250581 0 A ADDxPRS 4864 1.145 0.8671 0.3859 1.176e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9002 -0.8268 0.4083 7.927e-11
81 9 rs564398 0 C ADDxPRS 4864 1.111 0.8252 0.4092 9.87e-09
3 1 rs10914783 0 A ADDxPRS 4864 1.269 0.8226 0.4107 3.259e-06
66 9 rs10757264 0 G ADDxPRS 4864 0.9147 -0.7014 0.483 2.261e-07
6 1 rs599839 0 G ADDxPRS 4864 1.113 0.6864 0.4925 2.337e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.081 0.61 0.5418 1.24e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.08 0.6087 0.5427 7.32e-13
150 22 rs688034 0 T ADDxPRS 4864 1.083 0.5923 0.5536 1.124e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.078 0.5917 0.554 1.732e-12
99 9 rs2891168 0 A ADDxPRS 4864 1.078 0.5903 0.555 6.458e-13
147 21 rs2838756 0 C ADDxPRS 4864 1.077 0.5301 0.5961 2.747e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.941 -0.4787 0.6322 5.392e-10
126 16 rs7199903 0 T ADDxPRS 4864 0.9428 -0.4614 0.6445 2.201e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.9463 -0.4349 0.6636 1.317e-09
111 10 rs7910044 0 A ADDxPRS 4864 1.046 0.359 0.7196 3.375e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9611 -0.199 0.8423 3.249e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9747 -0.1793 0.8577 1.269e-05
54 8 rs16872634 0 C ADDxPRS 4864 0.9861 -0.09936 0.9209 4.173e-05
12 1 rs2133189 0 C ADDxPRS 4864 1.008 0.05463 0.9564 1.422e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.006 0.04582 0.9635 1.454e-05

p1.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 0.627 -2.3 0.02146 2.365e-05
36 5 rs449650 0 T ADDxPRS 4864 0.7442 -2.112 0.03473 6.285e-06
39 5 rs436495 0 A ADDxPRS 4864 0.7498 -2.069 0.03858 8.665e-06
42 5 rs565928 0 T ADDxPRS 4864 0.7573 -1.995 0.0461 6.79e-06
114 12 rs2398486 0 T ADDxPRS 4864 0.7194 -1.691 0.09087 3.565e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.8328 -1.515 0.1299 3.983e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.8041 -1.468 0.1421 2.865e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.144 1.17 0.2421 1.498e-09
87 9 rs10965219 0 G ADDxPRS 4864 0.8789 -1.117 0.2638 8.048e-11
60 9 rs523096 0 G ADDxPRS 4864 1.137 1.113 0.2658 1.457e-06
138 20 rs6071467 0 G ADDxPRS 4864 1.147 1.091 0.2751 3.571e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.135 1.09 0.2758 6.807e-14
135 19 rs7250581 0 A ADDxPRS 4864 1.162 1.058 0.2899 1.129e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.123 0.9969 0.3188 1.202e-13
123 16 rs12716963 0 G ADDxPRS 4864 1.153 0.9923 0.321 3.502e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.8828 -0.9631 0.3355 8.289e-06
96 9 rs4977574 0 A ADDxPRS 4864 1.116 0.9517 0.3412 7.259e-13
81 9 rs564398 0 C ADDxPRS 4864 1.115 0.9408 0.3468 9.849e-09
144 20 rs2093154 0 T ADDxPRS 4864 1.125 0.94 0.3472 3.189e-05
99 9 rs2891168 0 A ADDxPRS 4864 1.114 0.9323 0.3512 6.409e-13
120 14 rs10431700 0 G ADDxPRS 4864 1.114 0.9285 0.3531 3.365e-05
141 20 rs6071469 0 C ADDxPRS 4864 1.123 0.9196 0.3578 3.168e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.111 0.9103 0.3627 1.728e-12
150 22 rs688034 0 T ADDxPRS 4864 1.095 0.7419 0.4581 1.177e-05
6 1 rs599839 0 G ADDxPRS 4864 1.109 0.7366 0.4614 2.362e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9213 -0.7084 0.4787 2.289e-07
78 9 rs10965215 0 A ADDxPRS 4864 0.9241 -0.6838 0.4941 5.426e-10
3 1 rs10914783 0 A ADDxPRS 4864 1.189 0.6588 0.51 3.138e-06
75 9 rs7049105 0 G ADDxPRS 4864 0.9299 -0.6306 0.5283 1.319e-09
132 17 rs6502872 0 T ADDxPRS 4864 0.9354 -0.5836 0.5595 4.843e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9396 -0.5399 0.5893 2.369e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.053 0.4138 0.6791 2.817e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.036 0.2904 0.7715 1.706e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9666 -0.2614 0.7938 1.274e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9559 -0.2479 0.8042 3.235e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.019 0.1625 0.8709 3.273e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.012 0.09319 0.9258 4.153e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9942 -0.04525 0.9639 1.426e-05

p3.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 0.7796 -1.717 0.08594 2.235e-05
36 5 rs449650 0 T ADDxPRS 4864 0.8642 -1.441 0.1496 6.418e-06
39 5 rs436495 0 A ADDxPRS 4864 0.8654 -1.432 0.1521 8.793e-06
42 5 rs565928 0 T ADDxPRS 4864 0.8744 -1.329 0.184 6.9e-06
114 12 rs2398486 0 T ADDxPRS 4864 0.8322 -1.312 0.1896 3.418e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.8983 -1.231 0.2182 3.721e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.129 1.187 0.2354 1.039e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.098 1.114 0.2653 1.19e-13
87 9 rs10965219 0 G ADDxPRS 4864 0.9148 -1.079 0.2805 8.178e-11
84 9 rs7865618 0 G ADDxPRS 4864 1.087 1.017 0.3093 1.514e-09
96 9 rs4977574 0 A ADDxPRS 4864 1.087 0.9948 0.3198 7.234e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.085 0.9794 0.3274 6.386e-13
102 9 rs1333042 0 A ADDxPRS 4864 1.08 0.9235 0.3557 1.762e-12
93 9 rs6475606 0 C ADDxPRS 4864 1.078 0.8956 0.3705 6.751e-14
60 9 rs523096 0 G ADDxPRS 4864 1.071 0.8311 0.4059 1.486e-06
150 22 rs688034 0 T ADDxPRS 4864 1.073 0.8047 0.421 1.273e-05
6 1 rs599839 0 G ADDxPRS 4864 1.082 0.7806 0.4351 2.491e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9216 -0.771 0.4407 2.795e-05
81 9 rs564398 0 C ADDxPRS 4864 1.061 0.7169 0.4734 9.834e-09
120 14 rs10431700 0 G ADDxPRS 4864 1.059 0.6862 0.4926 3.296e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.9475 -0.6534 0.5135 5.519e-10
75 9 rs7049105 0 G ADDxPRS 4864 0.9523 -0.5922 0.5537 1.319e-09
21 2 rs2943634 0 A ADDxPRS 4864 1.052 0.5772 0.5638 2.151e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9626 -0.463 0.6434 2.58e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9584 -0.4585 0.6466 1.24e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.039 0.4204 0.6742 4.468e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9694 -0.3735 0.7088 2.384e-07
3 1 rs10914783 0 A ADDxPRS 4864 1.068 0.3395 0.7342 3.088e-06
12 1 rs2133189 0 C ADDxPRS 4864 0.9714 -0.3131 0.7542 1.393e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9751 -0.2689 0.788 8.699e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.9694 -0.2315 0.8169 3.151e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.019 0.216 0.829 2.85e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9843 -0.1913 0.8483 3.24e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.01 0.09561 0.9238 3.436e-05
144 20 rs2093154 0 T ADDxPRS 4864 1.008 0.08552 0.9318 3.108e-05
141 20 rs6071469 0 C ADDxPRS 4864 1.005 0.05938 0.9526 3.092e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.004 0.04957 0.9605 5.207e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9992 -0.008622 0.9931 3.473e-05

p1.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
39 5 rs436495 0 A ADDxPRS 4864 0.9179 -1.051 0.2934 8.77e-06
36 5 rs449650 0 T ADDxPRS 4864 0.9188 -1.035 0.3006 6.446e-06
135 19 rs7250581 0 A ADDxPRS 4864 1.088 1.017 0.3093 9.873e-06
9 1 rs2883720 0 T ADDxPRS 4864 0.9369 -0.9366 0.349 3.676e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9265 -0.9363 0.3491 6.874e-06
117 12 rs2167512 0 A ADDxPRS 4864 0.9009 -0.9091 0.3633 2.179e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.06 0.8739 0.3822 1.184e-13
150 22 rs688034 0 T ADDxPRS 4864 1.06 0.8394 0.4012 1.306e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9513 -0.7629 0.4455 8.06e-11
96 9 rs4977574 0 A ADDxPRS 4864 1.05 0.7312 0.4646 7.146e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.049 0.7218 0.4704 6.301e-13
114 12 rs2398486 0 T ADDxPRS 4864 0.9229 -0.7203 0.4714 3.324e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.047 0.6569 0.5112 2.313e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.044 0.6525 0.5141 1.776e-12
123 16 rs12716963 0 G ADDxPRS 4864 0.9477 -0.6524 0.5142 3.42e-05
6 1 rs599839 0 G ADDxPRS 4864 1.053 0.6372 0.524 2.615e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9574 -0.6123 0.5404 3.514e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9565 -0.6054 0.5449 1.203e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.038 0.5765 0.5643 1.513e-09
54 8 rs16872634 0 C ADDxPRS 4864 1.038 0.5183 0.6042 4.823e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9632 -0.5108 0.6095 1.358e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.033 0.4898 0.6243 6.693e-14
132 17 rs6502872 0 T ADDxPRS 4864 1.032 0.487 0.6262 5.464e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9675 -0.4647 0.6421 3.128e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.032 0.4636 0.6429 3.175e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9693 -0.4391 0.6606 3.144e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9736 -0.4077 0.6835 2.618e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.9751 -0.3838 0.7012 5.505e-10
60 9 rs523096 0 G ADDxPRS 4864 1.022 0.3262 0.7443 1.514e-06
75 9 rs7049105 0 G ADDxPRS 4864 0.979 -0.3246 0.7455 1.299e-09
81 9 rs564398 0 C ADDxPRS 4864 1.019 0.2866 0.7744 9.791e-09
18 2 rs17018897 0 G ADDxPRS 4864 0.9816 -0.2215 0.8247 2.798e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9855 -0.2213 0.8249 3.318e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.016 0.2083 0.835 8.704e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.9836 -0.1514 0.8797 3.072e-05
66 9 rs10757264 0 G ADDxPRS 4864 1.007 0.1038 0.9173 2.446e-07
3 1 rs10914783 0 A ADDxPRS 4864 1.007 0.04511 0.964 3.147e-06
147 21 rs2838756 0 C ADDxPRS 4864 1.002 0.02946 0.9765 2.817e-05

p3.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
9 1 rs2883720 0 T ADDxPRS 4864 0.922 -1.136 0.2559 3.556e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.07 0.9952 0.3197 5.545e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9415 -0.8246 0.4096 3.477e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.061 0.8239 0.41 2.55e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9335 -0.8156 0.4147 8.413e-06
105 9 rs1333048 0 A ADDxPRS 4864 1.057 0.8069 0.4198 1.111e-13
123 16 rs12716963 0 G ADDxPRS 4864 0.9353 -0.7955 0.4263 3.567e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9375 -0.7626 0.4457 6.227e-06
150 22 rs688034 0 T ADDxPRS 4864 1.052 0.7049 0.4808 1.335e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9423 -0.7038 0.4816 6.58e-06
15 1 rs17465637 0 T ADDxPRS 4864 0.9503 -0.6774 0.4982 1.214e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.046 0.6576 0.5108 6.82e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.046 0.6494 0.5161 6.013e-13
141 20 rs6071469 0 C ADDxPRS 4864 0.9559 -0.6189 0.536 3.077e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.049 0.6181 0.5365 8.62e-06
144 20 rs2093154 0 T ADDxPRS 4864 0.9575 -0.5952 0.5517 3.092e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9563 -0.5941 0.5524 1.374e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9615 -0.5808 0.5614 2.65e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.05 0.5701 0.5686 9.55e-06
6 1 rs599839 0 G ADDxPRS 4864 1.045 0.5295 0.5965 2.732e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.037 0.5222 0.6015 1.744e-12
87 9 rs10965219 0 G ADDxPRS 4864 0.9672 -0.4983 0.6183 7.453e-11
66 9 rs10757264 0 G ADDxPRS 4864 1.034 0.4862 0.6269 2.444e-07
120 14 rs10431700 0 G ADDxPRS 4864 1.025 0.3529 0.7242 3.046e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.021 0.3105 0.7562 6.47e-14
54 8 rs16872634 0 C ADDxPRS 4864 1.023 0.3087 0.7576 5.071e-05
147 21 rs2838756 0 C ADDxPRS 4864 0.9796 -0.2786 0.7805 2.785e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.024 0.2762 0.7824 2.826e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9766 -0.2079 0.8353 3.083e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9705 -0.1826 0.8551 3.179e-06
114 12 rs2398486 0 T ADDxPRS 4864 0.9816 -0.1622 0.8711 3.209e-05
81 9 rs564398 0 C ADDxPRS 4864 0.9902 -0.1455 0.8843 9.591e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.9917 -0.1233 0.9019 5.179e-10
117 12 rs2167512 0 A ADDxPRS 4864 0.9871 -0.1105 0.912 2.108e-05
60 9 rs523096 0 G ADDxPRS 4864 0.993 -0.1047 0.9166 1.516e-06
111 10 rs7910044 0 A ADDxPRS 4864 1.006 0.08698 0.9307 3.348e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.005 0.07814 0.9377 1.484e-09
75 9 rs7049105 0 G ADDxPRS 4864 0.9954 -0.06814 0.9457 1.212e-09

p1.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
9 1 rs2883720 0 T ADDxPRS 4864 0.8824 -1.502 0.133 3.449e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.11 1.315 0.1887 5.415e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.105 1.105 0.2691 8.347e-06
21 2 rs2943634 0 A ADDxPRS 4864 1.09 1.018 0.3085 2.364e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9337 -0.8689 0.3849 2.543e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.071 0.8492 0.3958 1.051e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.06 0.7237 0.4692 6.559e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.059 0.7125 0.4762 5.787e-13
138 20 rs6071467 0 G ADDxPRS 4864 0.9427 -0.6879 0.4915 3.44e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9485 -0.5993 0.549 1.227e-05
66 9 rs10757264 0 G ADDxPRS 4864 1.047 0.5776 0.5635 2.409e-07
39 5 rs436495 0 A ADDxPRS 4864 0.9455 -0.5696 0.569 7.953e-06
150 22 rs688034 0 T ADDxPRS 4864 1.048 0.5568 0.5777 1.339e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.046 0.5559 0.5783 1.703e-12
12 1 rs2133189 0 C ADDxPRS 4864 0.9561 -0.5098 0.6102 1.393e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.052 0.507 0.6122 2.9e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9529 -0.4901 0.6241 6.204e-06
147 21 rs2838756 0 C ADDxPRS 4864 0.9588 -0.4821 0.6297 2.773e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9607 -0.4688 0.6392 2.982e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9549 -0.4665 0.6408 5.916e-06
144 20 rs2093154 0 T ADDxPRS 4864 0.9626 -0.4457 0.6558 2.997e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9212 -0.4229 0.6724 3.271e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.9466 -0.4155 0.6778 3.261e-05
6 1 rs599839 0 G ADDxPRS 4864 1.041 0.4139 0.6789 2.765e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9704 -0.3835 0.7013 6.918e-11
111 10 rs7910044 0 A ADDxPRS 4864 1.029 0.3586 0.7199 3.265e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.029 0.3531 0.724 6.363e-14
123 16 rs12716963 0 G ADDxPRS 4864 0.9677 -0.3346 0.7379 3.711e-05
81 9 rs564398 0 C ADDxPRS 4864 0.9739 -0.3328 0.7393 9.44e-09
120 14 rs10431700 0 G ADDxPRS 4864 1.024 0.2962 0.7671 2.957e-05
60 9 rs523096 0 G ADDxPRS 4864 0.9839 -0.2061 0.8367 1.507e-06
117 12 rs2167512 0 A ADDxPRS 4864 1.029 0.2054 0.8373 2.058e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.018 0.2022 0.8398 5.199e-05
84 9 rs7865618 0 G ADDxPRS 4864 0.9859 -0.1805 0.8567 1.457e-09
75 9 rs7049105 0 G ADDxPRS 4864 1.007 0.08293 0.9339 1.142e-09
135 19 rs7250581 0 A ADDxPRS 4864 1.006 0.05887 0.9531 9.499e-06
78 9 rs10965215 0 A ADDxPRS 4864 1.002 0.02257 0.982 4.891e-10
114 12 rs2398486 0 T ADDxPRS 4864 1.002 0.01171 0.9907 3.114e-05

p3.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
9 1 rs2883720 0 T ADDxPRS 4864 0.8313 -1.857 0.06335 3.519e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.186 1.581 0.1139 8.254e-06
132 17 rs6502872 0 T ADDxPRS 4864 1.13 1.286 0.1984 5.217e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.8871 -1.266 0.2054 2.291e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.106 0.988 0.3232 1.868e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.092 0.9039 0.366 6.465e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.09 0.888 0.3745 5.707e-13
105 9 rs1333048 0 A ADDxPRS 4864 1.089 0.8819 0.3778 1.044e-13
102 9 rs1333042 0 A ADDxPRS 4864 1.076 0.7491 0.4538 1.676e-12
3 1 rs10914783 0 A ADDxPRS 4864 0.8555 -0.6629 0.5074 3.442e-06
93 9 rs6475606 0 C ADDxPRS 4864 1.061 0.61 0.5419 6.293e-14
138 20 rs6071467 0 G ADDxPRS 4864 0.9396 -0.6043 0.5456 3.523e-05
147 21 rs2838756 0 C ADDxPRS 4864 0.939 -0.601 0.5479 2.773e-05
66 9 rs10757264 0 G ADDxPRS 4864 1.052 0.5289 0.5969 2.357e-07
87 9 rs10965219 0 G ADDxPRS 4864 0.9546 -0.4939 0.6214 6.555e-11
111 10 rs7910044 0 A ADDxPRS 4864 1.048 0.4904 0.6239 3.238e-05
150 22 rs688034 0 T ADDxPRS 4864 1.048 0.4652 0.6418 1.242e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.936 -0.4268 0.6695 3.539e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9577 -0.4213 0.6735 3.043e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.96 -0.3982 0.6905 3.06e-05
39 5 rs436495 0 A ADDxPRS 4864 0.958 -0.3685 0.7125 7.758e-06
42 5 rs565928 0 T ADDxPRS 4864 0.9618 -0.3345 0.738 6.04e-06
120 14 rs10431700 0 G ADDxPRS 4864 1.032 0.3274 0.7434 2.962e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.038 0.3037 0.7614 2.899e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.972 -0.2688 0.7881 1.196e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.041 0.2395 0.8107 2.139e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9728 -0.2358 0.8136 5.757e-06
135 19 rs7250581 0 A ADDxPRS 4864 0.9725 -0.2329 0.8159 9.826e-06
54 8 rs16872634 0 C ADDxPRS 4864 1.022 0.2061 0.8367 5.291e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.983 -0.1622 0.8711 1.358e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.018 0.1539 0.8777 3.689e-05
6 1 rs599839 0 G ADDxPRS 4864 1.015 0.1328 0.8943 2.719e-05
81 9 rs564398 0 C ADDxPRS 4864 0.9874 -0.1325 0.8946 9.139e-09
84 9 rs7865618 0 G ADDxPRS 4864 0.9899 -0.1069 0.9149 1.399e-09
75 9 rs7049105 0 G ADDxPRS 4864 1.007 0.06867 0.9453 1.094e-09
60 9 rs523096 0 G ADDxPRS 4864 1.005 0.04821 0.9615 1.479e-06
78 9 rs10965215 0 A ADDxPRS 4864 1.001 0.0147 0.9883 4.671e-10
114 12 rs2398486 0 T ADDxPRS 4864 0.9992 -0.004684 0.9963 3.223e-05

p1.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
9 1 rs2883720 0 T ADDxPRS 4864 0.7929 -2.027 0.04262 3.856e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.237 1.72 0.08542 7.808e-06
126 16 rs7199903 0 T ADDxPRS 4864 0.8528 -1.453 0.1463 2.059e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.13 1.118 0.2635 5.04e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.122 1.028 0.3038 1.133e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.118 0.9971 0.3187 6.748e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.116 0.9809 0.3267 5.952e-13
3 1 rs10914783 0 A ADDxPRS 4864 0.7766 -0.9307 0.352 3.579e-06
102 9 rs1333042 0 A ADDxPRS 4864 1.099 0.8417 0.3999 1.709e-12
93 9 rs6475606 0 C ADDxPRS 4864 1.092 0.7948 0.4267 6.444e-14
147 21 rs2838756 0 C ADDxPRS 4864 0.9102 -0.7753 0.4382 2.767e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9229 -0.7349 0.4624 6.687e-11
135 19 rs7250581 0 A ADDxPRS 4864 0.9033 -0.7327 0.4637 1.029e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.076 0.6283 0.5298 1.375e-05
150 22 rs688034 0 T ADDxPRS 4864 1.064 0.5397 0.5894 1.142e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9401 -0.5199 0.6031 3.819e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.059 0.5144 0.607 3.334e-05
60 9 rs523096 0 G ADDxPRS 4864 1.054 0.4722 0.6368 1.479e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.064 0.4556 0.6487 3.503e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9474 -0.4556 0.6487 3.274e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9509 -0.4245 0.6712 3.294e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.044 0.3502 0.7262 5.076e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9409 -0.3451 0.73 3.516e-05
81 9 rs564398 0 C ADDxPRS 4864 1.035 0.3083 0.7579 9.238e-09
66 9 rs10757264 0 G ADDxPRS 4864 1.031 0.2809 0.7788 2.288e-07
12 1 rs2133189 0 C ADDxPRS 4864 1.03 0.2404 0.8101 1.334e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.026 0.2311 0.8172 2.965e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.021 0.1852 0.853 1.403e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.9832 -0.1551 0.8768 4.765e-10
15 1 rs17465637 0 T ADDxPRS 4864 1.018 0.1474 0.8828 1.173e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.9847 -0.1404 0.8883 1.118e-09
42 5 rs565928 0 T ADDxPRS 4864 0.9821 -0.1356 0.8921 6.334e-06
39 5 rs436495 0 A ADDxPRS 4864 0.9835 -0.125 0.9005 8.138e-06
117 12 rs2167512 0 A ADDxPRS 4864 1.02 0.1043 0.9169 2.24e-05
114 12 rs2398486 0 T ADDxPRS 4864 0.9836 -0.08951 0.9287 3.316e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.01 0.07201 0.9426 2.941e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9917 -0.06296 0.9498 2.604e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9981 -0.01434 0.9886 6.014e-06